Healthy Pumpkin Muffins
This post may contain affiliate links. See my disclosure policy.
My healthy pumpkin muffins are lightened up with less fat and sugar, but are every bit as moist and fluffy as you’d expect. They are quick and easy to make and perfect for a wholesome snack or afternoon treat.
Come fall, my healthy pumpkin muffin recipe becomes an almost weekly staple in my household. It’s the perfect use of pumpkin puree, uses wholesome ingredients, and is one of the few muffins my family begs me to make all the time.
When I was developing these (inspired by my healthy pumpkin bread), I tested them head-to-head with my classic pumpkin muffin recipe I showcased in culinary school (the kind loaded with butter and SO much sugar). Instead of white sugar, I like to use a little coconut sugar, which is less refined and keeps the muffins low sugar. I also swap out the white flour for oat flour, which adds extra protein, fiber, and whole grains. You could technically call these low-calorie pumpkin muffins, because each giant muffin has less than 150 calories – win!
Table of Contents
Why make my healthy pumpkin muffins
- Perfect texture and flavor. The texture is moist and fluffy in the middle with a tender crumb. They are full of pumpkin flavor, thanks to the addition of pumpkin puree to the batter (no pumpkin pie filling!).
- Tastes like bakery muffins. Don’t let the word ‘healthy’ fool you. My muffins taste like any good bakery-style muffin out there!
What readers are saying
★★★★★ – “These are delicious and super moist! They are so easy to make also!” – Adrienne
★★★★★ – “I love how wholesome they are. My kids love them for breakfast.” – Ollie from Facebook
Key Ingredients
Find the full printable recipe instructions and ingredient quantities below.
- Oat flour. Ground-up rolled or quick oats. Skip the expensive packaged kind and make your own with my homemade oat flour.
- Baking powder. The leavening agent gives the muffins some rise and fluffiness.
- Pumpkin spice. A must for any recipe using pumpkin puree. You can make your own by mixing ground cinnamon, nutmeg, cloves, and ground ginger.
- Pumpkin puree. Homemade pumpkin puree or unsweetened canned pumpkin. If you use the latter, be sure that it is NOT pumpkin pie filling.
- Coconut oil. A fantastic alternative to butter. Use refined coconut oil, as it has no coconut flavor whatsoever. You’ll notice that the amount used is much less than in other pumpkin muffins, which helps keep these relatively low-fat yet still moist and fluffy.
- Eggs. room temperature, please.
- Milk of choice. I used unsweetened almond milk to keep them dairy-free, but any milk can be used (such as coconut, soy, or non-fat milk).
- Coconut sugar. A refined sugar-free sweetener. You can find these at Asian grocers or health food stores. Of course, if you only have white or brown sugar, you can use that. I also tested these muffins with maple syrup and honey, and they work well.
- Oatmeal crumb topping. A simple mix of oat flour, rolled oats, sugar, cinnamon, and coconut oil.
Recipe variations
The beauty of these muffins lies in their ease of customization to suit a wide range of diets or preferences. Here is what I have tested:
- Make them vegan. Switch out the eggs for an egg substitute.
- Add mix-ins. Add chocolate chips to make healthy pumpkin chocolate chip muffins, or fold through some walnuts and pecans for some crunch.
- Add applesauce. Replace half the pumpkin with unsweetened applesauce. This gives the muffins a slightly less intense pumpkin flavor while keeping them perfectly moist and fluffy.
- Add banana. Swap out half the pumpkin for mashed banana.
- Pumpkin oatmeal muffins. Do as I did and add a simple oatmeal streusel topping. Combine rolled oats with coconut sugar and sprinkle the mixture on top of each muffin before baking. Drizzle with a simple powdered sugar glaze.
How to make healthy pumpkin muffins
Step 1- Make the batter. Whisk together your flour, baking powder, and pumpkin pie spice in a small bowl, then set that aside. In a mixing bowl, whisk together the remaining ingredients until creamy.
Step 2- Combine. Gently fold the dry ingredients into the wet ingredients until fully incorporated, with no air pockets remaining.
Step 3- Make the crumb topping. If desired, make the crumb topping by mixing the oat flour, rolled oats, coconut sugar, cinnamon, and coconut oil.
Step 4- Bake the muffins. Disperse the batter evenly amongst a greased 12-count muffin tin and sprinkle the crumb topping over each one. Bake the muffins for 18-20 minutes or until a skewer comes out mostly clean.
Arman’s recipe tips
- Do not over-bake the muffins. Remember, muffins will continue to bake as they are cooling in the muffin tin. Remove them from the oven when a toothpick comes out mostly clean.
- Use a wire rack. Cool the muffins in the tin for 10 minutes then move them to a wire rack. My first test batch turned soggy on the bottom when I left them in the tin too long.
- Use superfine oat flour. For the best texture of the muffins, the oat flour used must be of a powdery texture. Some brands, like Bob’s Red Mill, are great, but others are a little coarser, so I suggest blending them down even further to a fine powder.
- Adjust the sweetness. These muffins are pleasantly sweet, thanks to the addition of coconut sugar and the natural sweetness of the pumpkin. However, if you prefer a sweeter muffin, add an extra tablespoon or two of coconut sugar.
- Use actual flour. If you prefer muffins made with baking flour, swap out the oat flour with whole wheat flour.
Storage instructions
To store: Muffins can be stored at room temperature, covered, for up to 3 days. If you’d like them to keep longer, store them in the refrigerator and they will keep for up to 1 week.
To freeze: Place muffins in a ziplock bag and store them in the freezer for up to 6 months. Let them thaw completely from their frozen state.
Frequently asked questions
If your pumpkin muffins are more on the dense side, it comes down to how long you cook them! To ensure they are never dense, be sure to remove them from the oven when a toothpick comes out mostly clean.
In my testing, gummy muffins usually came down to two things: pulling them from the oven too early or using oat flour that was too coarse. The first few batches I made with supermarket oat flour were heavier, but when I blended my own oats into a very fine powder, the crumb was much lighter and fluffier. A quick tip: aim for an internal temp of around 190°F to know they’re fully baked.
Yes, but it does change the flavor and texture. I tested these with half the coconut sugar, and while they still rose nicely, the pumpkin flavor felt a little flat. My compromise is to bake them as written and keep the muffins plain (no glaze or crumb topping) if I want them less sweet. That way, you keep the moisture and structure without losing all the flavor.
Absolutely. I’ve baked them both ways, and while the crumb adds a lovely crunch and bakery-style look, the muffins themselves are still moist and tender without it. When I skip the topping, I sometimes fold in a handful of chopped walnuts or pecans for that bit of texture instead.
✅ Nutrition reviewed
Since these muffins discuss caloric count and health benefits, the nutrition information has been reviewed by registered dietitian Felicia Newell, MScAHN, RD, CPT.
Healthy Pumpkin Muffins
Video
Ingredients
- 3 cups oat flour gluten free, if needed
- 1 teaspoon baking powder
- 1 1/2 teaspoons pumpkin pie spice
- 2 cups pumpkin puree 15 oz can
- 1/4 cup coconut oil melted
- 2 large eggs
- 2 tbsp unsweetened almond milk any milk works
- 1 cup coconut sugar
Crumb topping
- 3 tablespoons oat flour
- 3 tablespoons rolled oats
- 1 tablespoon coconut sugar
- 1/4 teaspoon cinnamon
- 2 1/2 tablespoons coconut oil melted
Instructions
- Preheat the oven to 180C/350F. Grease a 12-count muffin tin and fill each one with muffin liners.
- In a small bowl, whisk together the oat flour, baking powder, and pumpkin pie spice and set aside. In a separate mixing bowl, add the pumpkin puree, eggs, coconut oil, milk, and coconut sugar and mix until smooth.
- Gently fold the dry ingredients into the wet ingredients, mixing until combined. Distribute the batter evenly amongst the muffin tin.
- Make the crumb topping by mixing together the oat flour, rolled oats, coconut sugar, cinnamon, and melted coconut oil. Sprinkle over the top of each muffin.
- Bake the muffins for 18-20 minutes, or until a toothpick comes out mostly clean.
- Remove the muffins from the oven and let them cool in the tin for 10 minutes, before carefully transferring them to a wire rack to cool completely.
I make these healthy pumpkin muffins every time I need to use up canned pumpkin, and they are always a hit with my family.
Love these healthy pumpkin muffins! so moist and tender.
I need to try this. Just need to buy all imgredients.
On your photo they look so nice. Just the time for eating pumpkins-autumn!
Could you use avacado oil and or almond flour?
Only tried it as written 🙂
Tried this recipe, it was really good, but the only thing that I thought was too much of that ingredient is the pumpkin, I know that it’s called pumpkin muffins, but it just was too dense. It felt like a heavy muffin.
But still it was good.
Simple easy and delicious recipe!